GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_molyb - Oxidoreductase molybdopterin binding domain
Pfam: PF00174 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 169
Sequences: 2086
Seq/Len: 12.34
HH_delta: 0.061 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
39_Q122_Y0.97853.549
72_P75_D0.908713.296
30_T33_D0.795422.885
24_E81_G0.74752.711
20_S155_R0.709912.575
41_T69_T0.703122.550
20_S157_E0.702222.547
24_E83_K0.685632.487
91_F156_I0.679322.464
92_T155_R0.662622.403
18_T28_T0.628362.279
69_T123_E0.626242.271
41_T67_E0.611032.216
16_T28_T0.567832.059
27_L80_A0.556152.017
37_L79_K0.554232.010
66_A124_M0.529851.922
78_E114_L0.525971.908
121_A140_V0.508071.843
76_L120_L0.501721.820
46_L146_G0.494181.792
77_L158_V0.48991.777
91_F153_V0.483861.755
67_E126_G0.467071.694
74_S78_E0.465891.690
75_D78_E0.454191.647
90_V159_T0.446211.618
22_L160_D0.442071.603
22_L83_K0.43551.580
45_T65_N0.435271.579
39_Q69_T0.431111.564
120_L153_V0.430731.562
73_L113_A0.420391.525
92_T157_E0.402091.458
46_L149_S0.397141.440
18_T155_R0.391771.421
89_V158_V0.391541.420
85_D160_D0.382531.387
94_A154_S0.381731.385
90_V157_E0.378921.374
120_L137_L0.371661.348
29_L79_K0.364181.321
118_V141_V0.362091.313
108_L141_V0.360711.308
43_T67_E0.357571.297
140_V149_S0.355451.289
71_V76_L0.349711.268
23_V26_P0.339881.233
164_P168_E0.3341.211
115_E118_V0.327541.188
93_G150_V0.327021.186
165_G168_E0.323371.173
106_V147_Y0.322271.169
15_W31_L0.315491.144
35_K128_P0.312251.133
27_L79_K0.311371.129
37_L71_V0.307491.115
109_P112_D0.307051.114
89_V113_A0.304771.105
112_D144_K0.30091.091
31_L35_K0.300551.090
39_Q123_E0.297691.080
22_L85_D0.293771.065
46_L66_A0.290041.052
35_K122_Y0.288431.046
32_A36_A0.288391.046
40_V72_P0.287651.043
75_D79_K0.286871.040
23_V80_A0.284311.031
123_E128_P0.279271.013
22_L86_A0.278471.010
36_A79_K0.278051.008
19_V23_V0.276591.003
141_V149_S0.276121.001
106_V148_R0.276091.001
86_A158_V0.274160.994
82_I110_L0.271390.984
91_F139_L0.271230.984
21_G26_P0.269140.976
34_L137_L0.262180.951
67_E125_N0.261580.949
33_D36_A0.259680.942
49_V147_Y0.258910.939
124_M130_P0.25860.938
87_K160_D0.258050.936
25_N81_G0.257710.935
73_L139_L0.252940.917
17_L137_L0.252860.917
50_G58_W0.249060.903
13_E32_A0.248570.902
47_H106_V0.247950.899
89_V156_I0.246380.894
90_V168_E0.244450.887
139_L150_V0.236060.856
106_V168_E0.229070.831
73_L156_I0.228260.828
122_Y137_L0.227580.825
49_V145_Y0.226540.822
112_D143_G0.22580.819
37_L75_D0.22490.816
73_L76_L0.222960.809
16_T30_T0.22190.805
13_E31_L0.21870.793
34_L71_V0.218420.792
32_A35_K0.217740.790
20_S26_P0.215980.783
90_V164_P0.215080.780
147_Y168_E0.212260.770
71_V122_Y0.209640.760
77_L82_I0.208530.756
45_T50_G0.206980.751
145_Y148_R0.206890.750
40_V75_D0.205070.744
69_T122_Y0.203830.739
91_F104_Y0.203690.739
34_L122_Y0.203290.737
50_G144_K0.199810.725
66_A125_N0.199220.723
42_Q119_I0.198970.722
77_L113_A0.198230.719
106_V150_V0.198150.719
19_V27_L0.194740.706
71_V75_D0.194620.706
35_K123_E0.193710.703
49_V167_W0.193330.701
38_P75_D0.191490.695
159_T163_S0.191080.693
112_D115_E0.188820.685
50_G147_Y0.186350.676
72_P119_I0.186050.675
90_V105_S0.185470.673
23_V158_V0.184710.670
15_W137_L0.184050.668
74_S116_E0.183210.664
144_K148_R0.182190.661
115_E143_G0.179980.653
17_L34_L0.179360.651
45_T59_S0.178880.649
39_Q71_V0.178540.648
71_V120_L0.176890.642
133_H138_R0.174450.633
116_E119_I0.173290.629
128_P135_G0.172990.627
23_V27_L0.172350.625
129_L134_G0.171510.622
68_W121_A0.171420.622
68_W138_R0.171080.620
47_H50_G0.170290.618
48_C134_G0.170270.618
137_L153_V0.168760.612
88_Y162_E0.168360.611
49_V148_R0.167980.609
121_A139_L0.164890.598
139_L153_V0.164620.597
148_R167_W0.162910.591
104_Y148_R0.1620.588
161_E164_P0.161030.584
105_S165_G0.160790.583
117_D143_G0.160730.583
94_A135_G0.159990.580
25_N161_E0.159640.579
23_V86_A0.159460.578
95_D124_M0.158810.576
119_I140_V0.158460.575
29_L80_A0.158390.574
109_P144_K0.157550.571
107_S147_Y0.157310.571
24_E27_L0.157180.570
81_G158_V0.156860.569
13_E35_K0.156360.567
113_A118_V0.155690.565
47_H144_K0.155060.562
17_L29_L0.154890.562
27_L33_D0.154450.560
150_V168_E0.154150.559
153_V156_I0.153890.558
49_V144_K0.153790.558
14_S84_P0.153730.558
110_L158_V0.15350.557
82_I158_V0.152120.552
21_G24_E0.151930.551
25_N78_E0.15080.547
47_H147_Y0.150460.546
43_T65_N0.149820.543
82_I114_L0.149810.543
73_L118_V0.149740.543
21_G86_A0.148830.540
18_T22_L0.148770.540
113_A116_E0.148390.538
19_V76_L0.148110.537
90_V163_S0.147550.535
20_S28_T0.147370.535
28_T33_D0.147010.533
16_T127_E0.146770.532
148_R168_E0.145710.528
120_L139_L0.14570.528
40_V119_I0.145590.528
21_G25_N0.144920.526
60_A66_A0.144870.525
134_G151_K0.144820.525
88_Y148_R0.144590.524
84_P110_L0.144470.524
147_Y165_G0.144320.523
25_N79_K0.143910.522
108_L144_K0.143890.522
51_N143_G0.143470.520
94_A153_V0.142920.518
68_W135_G0.142890.518
105_S150_V0.142360.516
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1ogpA0.99411000.061
2blfA0.99411000.068
2a9dA0.98821000.069
1soxA0.98821000.072
2xtsA0.94671000.074
2bihA0.98221000.08
2biiA0.98221000.08
1xdyA0.93491000.139
3iwhA0.603636.20.938
3gk5A0.591728.30.941

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